How Does a Protein Skimmer Work? - A Simple Explanation

Welcome to Simple Reefs. This is a brand new website dedicated to taking the complexity out of Marine Aquarium Ownership. Our goal is to show you how you can own your very own slice of the ocean without spending a fortune. As well as giving you tons of easy to digest information on all things marine. Today, we are going to try to answer a question that, I am sure, many new hobbyists have. How does a protein skimmer work?

If you have missed any of our previous articles on protein skimmers, feel free to click on the links below. We are aiming to get you fully clued up on what protein skimmers are and how they work. As well as telling you whether you need one in your aquarium and what are the pros and cons.

• What is a protein skimmer and What Do They Do?
• What are the benefits of a protein skimmer?
• What are the downsides of a protein skimmer?
• Do you need a protein skimmer in your marine aquarium?

We briefly explained that a protein skimmer produces thousands of tiny air bubbles to trap waste in our article on what a protein skimmer does. But, in this article, we are going to go into a little more detail on just how this process takes place and what the science is behind it. This is Simple Reefs so I am going to try to keep it as easy to understand as possible.

Removing Waste Before it Rots

There is, obviously, a much more technical explanation for this process than what I am going to offer here. After all, Simple Reefs is designed to keep marine aquarium stuff simple. I do see a few major websites getting this process a little bit confused, however, so I hope I can clear this up a bit.

A protein skimmer recreates the natural process of foam fractionation to remove dissolved organic matter from the water. In less complex terms, a protein skimmer utilises foam to trap and remove organic waste from the aquarium’s water column. After all, our aquariums are, what is known as, a closed system. Meaning the nutrients don’t have any way of escaping and will, over time, accumulate.

With this in mind, we need to get rid of them. There are a number of ways of doing this but most of those methods target the waste, either, before it has broken down and is in solid form, or, after it has already been processed and turned into nitrates.

That’s pretty inefficient, though. What about all those oils, proteins and fats that are left to dissolve into the water? They are going to turn into nitrates, too, and add to the nutrient load of our aquarium. But what if we could remove them before they had a chance to rot? Well, that’s where a protein skimmer comes in.

How Does a Protein Skimmer Work?

The idea behind a protein skimmer is that many of the unwanted organic molecules (the fats and proteins) floating around in our water have a particular trait, regarding electrical polarity, that can be utilised to our advantage.

They are hydrophobic which means they hate water but are quite partial to a bit of air. Along with those, there are other, typically larger, molecules that are attracted to water on one side and to air on the other side (Amphipathic). We can use this attraction to air against these waste molecules but we are going to need some bubbles to do it.

That is where a protein skimmer comes in and they are designed specifically for this task. The protein skimmer has, typically, a wide bottom and a narrow neck. It pulls our aquarium’s water through the bottom of its body into what is known as a “reaction chamber”. This is where the magic takes place. As the water is drawn in, air is injected into the water through a tube.

Most modern skimmers will have a pump fitted with a needle impeller which will spin at high speed and churn the aerated water up to make bubbles. You also have different types of skimmers which achieve this result in different ways. For example, a venturi skimmer will force the water through a constricted area, along with the air, to create bubbles.

This aerated water may then go through a grid with lots of holes called a bubble plate. Again, each protein skimmer may be different. Those aerated bubbles, in the water, will then accumulate in the narrower neck area of the skimmer. This creates a surface consisting of thousands of these tiny bubbles. The smaller the bubble size, the better, as smaller bubbles are less likely to burst and a higher rate of bubbles creates a more stable surface for the next step to take place.

The air in the water has nowhere to go but up so the bubbles begin to climb. Remember how we talked about those molecules that we want to remove from our water? The amphipathic ones that have a water loving side and an air loving side and the hydrophobic molecules that hate water and love air? Well, we are going to give them exactly what both of them want – Air!

The Power of Bubbles

This air and water interaction now taking place in the reaction chamber of our skimmer will, basically, attract all of those molecules. After all, our air bubbles are giving them exactly what they want – air. The hydrophobic molecules are there for the air, alone, so will head straight for the bubbles where they will be trapped. The amphipathic molecules will act a little differently. Basically shoving their air loving faces into the bubbles and leaving their water loving butts sticking out into the water. Either way, as long as the integrity of our bubbles remain, they can’t move.

This is where surface tension comes in. The more bubbles we create, the more surface tension we have and the more solidly we can hold these unwanted molecules. The bubbles will now do what bubbles do and rise up the neck of the skimmer, carrying all of those unwanted molecules with them. Almost like each bubble is a tiny set of hands lifting them and passing them to the top. These bubbles will hold onto the molecules, preventing them from escaping back into the water.

The bubbles closer to the top of the skimmer’s neck will begin to grow larger. Eventually pushing the molecules right up into the neck of the skimmer’s collection cup where they will overflow as a thick, awful smelling, airy foam known as skimmate. Eventually ending up in the collection cup itself.

The clean water left will flow back down the neck and into the tank. These proteins and fats can no longer rot in our tanks because we are going to throw them down the toilet (likely gagging from the smell while we do it). This process will continue indefinitely as long as your skimmer is running. Naturally, this is a very basic description and I am no super smart science guy so I can only explain from my point of understanding.

Seem Familiar?

Now, all this talk of saltwater and awful smelling foam might ring a few bells, for you. There’s a reason for that. I grew up in a seaside town and spent a lot of time at the beach, which was pretty cool, aside from the horribly poverty and lack of tourism. Heading out to the beach, a common site would be thick foam all over the place where the tide was rolling in.

Naturally, as kids do. My friends, and me, made some crude jokes about where this foam came from. Hilarious, as I am sure you can guess. In reality, the foam, actually, originates from that phrase we mentioned earlier – foam fractionation. This completely natural process is extremely close to what we are discussing here. In fact, it is pretty much the exact same thing which explains why that foam smells so bad, especially on sunny days.

This sea foam you see at the beach is, basically, made up of these same air loving waste molecules that we are trying to remove from our marine aquarium. The foam contains tons of dissolved organic matter that has been attracted to the air forming in the water as it laps the shore. That process is the exact same thing we are recreating in our marine aquariums to help keep them clean. Whereas the sea is an open system capable of managing nutrients organically. We can’t do that in our closed systems so we give it a little help.

Wet or Dry?

This is a phrase you will have heard a number of times regarding protein skimmers. You can either run them wet or dry. But what exactly does it mean? Well, it’s really very straight forward. Wet simply means that you are adjusting your protein skimmer to have more water in the reaction chamber relative to the foam. A wet protein skimmer will only have a rather short layer of bubbles at the top of the neck. Running a protein skimmer dry means you will have less water in the reaction chamber and lots of bubbles.

But why do we do this? Well, a wet protein skimmer will process more water and produce a more diluted foam. This means you are skimming at a faster rate but each time you fill the cup there will be less concentrated waste in the collection cup. Skimming dry will take much longer to fill the cup and will remove waste slower but the resulting skimmate will be more concentrated and contain a lot more matter. Skimming wet can drop your water level faster but is useful in a crisis.

Skimming wet may be more efficient if you need cleaner water as the waste will be processed in a speedier manner. If you don’t mind a bit of dirt or have soft coral, skimming dry might be the better option. The Goldilocks level is somewhere in between, however. Slightly wet but dry enough to produce a well concentrated level of skimmate.

In Short

To summarise, we use protein skimmers to remove dissolved organic waste from our aquariums via a process known as foam fractionation. The waste molecules are attracted, at least partially, to air and head towards the air bubbles created by our skimmer. The bubbles trap the molecules and then rise through the skimmer’s neck, into a collection cup, where we can remove them. Pretty simple. Thank you very much for reading.